MDO test case: hyperparathyroidism

[cmungall]

Consider the phenotype parathyroidism and its occurrence in various diseases: http://www.monarchinitiative.org/phenotype/HP:0000843 (click 'disease' tab)

These are the types of DC:0000201 'hyperparathyroidism'

• OMIM:145000 ! HYPERPARATHYROIDISM 1
• OMIM:145001 ! HYPERPARATHYROIDISM 2
• OMIM:239200 ! Hyperparathyroidism, Neonatal Severe Primary
• OMIM:600166 ! Hyperparathyroidism, Primary, Caused By Water Clear Cell Hyperplasia
• OMIM:610071 HYPERPARATHYROIDISM 3

One might think we can use 'hallmark' to cluster diseases. However, the hallmark qualifier is lacking from phenotype association for the phenotype hyperparathyroidism for the above diseases.

For comparison, Orphanet classifications of OMIMs:

• OMIM:145000 ! HYPERPARATHYROIDISM 1 Orphanet:99877 ! Familial parathyroid adenoma,Orphanet:99879 ! Familial isolated hyperparathyroidism
• OMIM:145001 ! HYPERPARATHYROIDISM 2 Orphanet:99880 ! Hyperparathyroidism - jaw tumor syndrome
• OMIM:239199 ! Hyperparathyroidism, Neonatal Self-Limited Primary, with Hypercalciuria NOT-IN-ORDO
• OMIM:239200 ! Hyperparathyroidism, Neonatal Severe Primary Orphanet:417 ! Neonatal severe primary hyperparathyroidism
• OMIM:256120 ! Nephropathy, Deafness, and Hyperparathyroidism Orphanet:2668 ! Nephropathy - deafness - hyperparathyroidism
• OMIM:600166 ! Hyperparathyroidism, Primary, Caused By Water Clear Cell Hyperplasia Orphanet:99878 ! Primary parathyroids hyperplasia
• OMIM:612089 ! Hypophosphatemic Rickets And Hyperparathyroidism NOT-IN-ORDO

To complicate matters, it seems we have no annotations for OMIM:610071 HYPERPARATHYROIDISM 3 (hence it doesn't show up above)

[pnrobinson]

Note that we have only used frequency annotations such as hallmark if there is data to this effect. Clearly, hyperparathyroidism is essential to many of these diseases. But this (and many other things) will require careful biocuration, and should be something that we achieve over the next 5 years. Note that as it stands "hallmark" is used only for the frequency, and thereby only indirectly to indicate whether a feature is essential for the disease definition. -peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universit�t Berlin Institut f�r Medizinische Genetik und Humangenetik Charit� - Universit�tsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

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Von: Chris Mungall [notifications@github.com] Gesendet: Montag, 9. M�rz 2015 02:07 An: monarch-initiative/human-disease-ontology Betreff: [human-disease-ontology] MDO test case: hyperparathyroidism (#8)

Consider the phenotype parathyroidism and its occurrence in various diseases: http://www.monarchinitiative.org/phenotype/HP:0000843 (click 'disease' tab)

These are the types of DC:0000201 'hyperparathyroidism'

• OMIM:145000http://monarchinitiative.org/disease/OMIM_145000 ! HYPERPARATHYROIDISM 1
• OMIM:145001http://monarchinitiative.org/disease/OMIM_145001 ! HYPERPARATHYROIDISM 2
• OMIM:239200http://monarchinitiative.org/disease/OMIM_239200 ! Hyperparathyroidism, Neonatal Severe Primary
• OMIM:600166http://monarchinitiative.org/disease/OMIM_600166 ! Hyperparathyroidism, Primary, Caused By Water Clear Cell Hyperplasia

One might think we can use 'hallmark' to cluster diseases. However, the hallmark qualifier is lacking from phenotype association for the phenotype hyperparathyroidism for the above diseases.

For comparison, Orphanet classifications of OMIMs:

• OMIM:145000http://monarchinitiative.org/disease/OMIM_145000 ! HYPERPARATHYROIDISM 1 Orphanet:99877http://monarchinitiative.org/disease/Orphanet_99877 ! Familial parathyroid adenoma,Orphanet:99879http://monarchinitiative.org/disease/adenoma,Orphanet_99879 ! Familial isolated hyperparathyroidism
• OMIM:145001http://monarchinitiative.org/disease/OMIM_145001 ! HYPERPARATHYROIDISM 2 Orphanet:99880http://monarchinitiative.org/disease/Orphanet_99880 ! Hyperparathyroidism - jaw tumor syndrome
• OMIM:239199http://monarchinitiative.org/disease/OMIM_239199 ! Hyperparathyroidism, Neonatal Self-Limited Primary, with Hypercalciuria
• OMIM:239200http://monarchinitiative.org/disease/OMIM_239200 ! Hyperparathyroidism, Neonatal Severe Primary Orphanet:417http://monarchinitiative.org/disease/Orphanet_417 ! Neonatal severe primary hyperparathyroidism
• OMIM:256120http://monarchinitiative.org/disease/OMIM_256120 ! Nephropathy, Deafness, and Hyperparathyroidism Orphanet:2668http://monarchinitiative.org/disease/Orphanet_2668 ! Nephropathy - deafness - hyperparathyroidism
• OMIM:600166http://monarchinitiative.org/disease/OMIM_600166 ! Hyperparathyroidism, Primary, Caused By Water Clear Cell Hyperplasia Orphanet:99878http://monarchinitiative.org/disease/Orphanet_99878 ! Primary parathyroids hyperplasia
• OMIM:612089http://monarchinitiative.org/disease/OMIM_612089 ! Hypophosphatemic Rickets And Hyperparathyroidism

� Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/human-disease-ontology/issues/8.

[drseb]

Hi,

I just checked some of the examples:

• OMIM:145000http://monarchinitiative.org/disease/OMIM_145000 ! HYPERPARATHYROIDISM 1 Orphanet:99877http://monarchinitiative.org/disease/Orphanet_99877 ! Familial parathyroid adenoma,Orphanet:99879http://monarchinitiative.org/disease/adenoma,Orphanet_99879 ! Familial isolated hyperparathyroidism

Orphanet has no clinical signs for these 2.

• OMIM:145001http://monarchinitiative.org/disease/OMIM_145001 ! HYPERPARATHYROIDISM 2 Orphanet:99880http://monarchinitiative.org/disease/Orphanet_99880 ! Hyperparathyroidism - jaw tumor syndrome

Orphanet has no clinical signs for this.

• OMIM:239200http://monarchinitiative.org/disease/OMIM_239200 ! Hyperparathyroidism, Neonatal Severe Primary Orphanet:417http://monarchinitiative.org/disease/Orphanet_417 ! Neonatal severe primary hyperparathyroidism

This should be in your data, if you use our annotation data (not sure if). My pipeline produces the following line in phenotype_annotation.tab: OMIM 239200 HYPERPARATHYROIDISM, NEONATAL SEVERE PRIMARY HP:0000843 ORPHANET:417 TAS hallmark O NEONATAL SEVERE PRIMARY HYPERPARATHYROIDISM|NSHPT|http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=417 2015.03.09 orphanet

Please note, that their disease mapping data is not always perfect. I ended up with the solution to only include Orphanet -> OMIM mapping, iff there is exactly one OMIM entry mapped. I can explain more if we manage to get a Skype-call for this and other topics soon.

Best, Seb

[cmungall]

This issue was moved to monarch-initiative/monarch-disease-ontology#12